SNU Compbio Lab
Bulletin of the Korean Chemical Society
- A benchmark study of machine learning methods for molecular electronic transition: Tree-based ensemble learning versus graph neural network
- Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA
- Conformational Sampling of Flexible Ligand-binding Protein Loops
- Structural Basis of Functional Conversion of a Floral Repressor to an Activator: A Molecular Dynamics Simulation Study
- Efficiency of Rotational Operators for Geometric Manipulation of Chain Molecules
Journal of Chemical Information and Modeling
- GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network
- GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential
- Prediction of Molecular Electronic Transitions Using Random Forests
- GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds
- GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors
- Evaluation of GalaxyDock Based on the Community Structure–Activity Resource 2013 and 2014 Benchmark Studies
- GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains
Journal of Chemical Theory and Computation
- Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies
- Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane
- Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy
- Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations
Journal of Computational Chemistry
- GalaxyDock2-HEME: protein-ligand docking for heme proteins
- Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design
- GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility
- GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters
- GalaxyDock2: Protein–ligand docking using beta-complex and global optimization
- LigDockCSA: Protein–ligand docking using conformational space annealing
- Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller
- Using quaternions to calculate RMSD
- A kinematic view of loop closure
Journal of Computer-Aided Molecular Design
- GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
- Absolute binding free energies for octa-acids and guests in SAMPL5
- Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge
Journal of Physical Chemistry B
- Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane
- Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation
- Strength of Cα−H···O=C Hydrogen Bonds in Transmembrane Proteins
Methods in Molecular Biology
- Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. In "Protein Structure Prediction"
- Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock. In "Modeling Peptide-Protein Interactions"
- Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers. In "Computational Design of Ligand Binding Proteins"
Nucleic Acids Research
- HProteome-BSite: predicted binding sites and ligands in human 3D proteome
- GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
- GalaxyRefine2: Simultaneous refinement of inaccurate local regions and overall protein structure
- GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure
- Galaxy7TM: Flexible GPCR-ligand docking by structure refinement
- GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
- GalaxySite: ligand-binding-site prediction by using molecular docking
- GalaxyRefine: protein structure refinement driven by side-chain repacking
- GalaxyWEB server for protein structure prediction and refinement
- The FALC-Loop web server for protein loop modeling
Proteins
- Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment
- Protein oligomer structure prediction using GALAXY in CASP14
- Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment
- Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges
- Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45
- Prediction of protein oligomer structures using GALAXY in CASP13
- Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment
- Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning
- Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment
- The challenge of modeling protein assemblies: the CASP12-CAPRI experiment
- Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30
- Effective protein model structure refinement by loop modeling and overall relaxation
- Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
- Blind prediction of interfacial water positions in CAPRI
- Community-wide evaluation of methods for predicting the effect of mutations on protein–protein interactions
- Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors
- New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies
- Refinement of unreliable local regions in template-based protein models
- Refinement of protein termini in template-based modeling using conformational space annealing
- De novo protein structure prediction by dynamic fragment assembly and conformational space annealing
- Protein loop modeling by using fragment assembly and analytical loop closure
- A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
others
ACS Catalysis
ACS Omega
Angewandte Chemie International Edition
- Switchable Nanoporous Sheets by the Aqueous Self-Assembly of Aromatic Macrobicycles
- Self-Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles
BMC Bioinformatics
- GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
Biochemistry
Biodesign
- Accurate protein structure prediction: what comes next?
- Prediction of Protein Structure and Interaction by GALAXY Protein Modeling Programs
Bioinformatics
Biophysical Journal
Chemical Science
Chemosphere
Communications Biology
Computational and Structural Biotechnology Journal
- Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction
- CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking
Current Opinion in Structural Biology
EMBO Molecular Medicine
European Journal of Medicinal Chemistry
Human Mutation
Inflammatory Bowel Diseases
International Journal of Quantum Chemistry
Journal of Biological Chemistry
- A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae
- Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface
Journal of Chemical Physics
Journal of Molecular Biology
- GalaxyDomDock: An ab initio domain–domain docking web server for multi-domain protein structure prediction
- Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
Journal of the Korean Physical Society
Molecular Biology
Nature Communications
- Structural basis of neuropeptide Y signaling through Y1 receptor
- Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains
PLoS ONE
Physical Chemistry Chemical Physics
Proceedings of the National Academy of Sciences
Protein Science
- Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif
- The flexibility in the proline ring couples to the protein backbone
Science
Scientific Reports
- An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
- GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking